Merge branch 'master' into core-updates

1 files changed, 335 insertions, 67 deletions

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ba9153b68b..3bd6710667 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -43,6 +43,7 @@
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017 Kei Kebreau <kei@openmailbox.org>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -100,6 +101,7 @@
   #:use-module (gnu packages qt)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sdl)
+  #:use-module (gnu packages search)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages statistics)
@@ -655,26 +657,50 @@ on localhost.")
 (define-public python-pytz
   (package
     (name "python-pytz")
-    (version "2016.10")
+    (version "2017.2")
     (source
      (origin
       (method url-fetch)
-      (uri (pypi-uri "pytz" version ".tar.bz2"))
+      (uri (pypi-uri "pytz" version ".zip"))
       (sha256
        (base32
-        "0az099cyp6p5xbsvfcdacj4hvxncbwm2ayn3h55mcp07zb2b45kh"))))
+        "12cmd3j46d2gcw08bspvp6s9icfcvx88zjz52n1bli9dyvl5dh7m"))))
     (build-system python-build-system)
-    (arguments `(#:tests? #f)) ; no test target
+    (native-inputs
+     `(("unzip" ,unzip)))
     (home-page "http://pythonhosted.org/pytz")
     (synopsis "Python timezone library")
-    (description
-     "This library allows accurate and cross platform timezone calculations
-using Python 2.4 or higher and provides access to the Olson timezone database.")
+    (description "This library brings the Olson tz database into Python.  It
+allows accurate and cross platform timezone calculations using Python 2.4 or
+higher.  It also solves the issue of ambiguous times at the end of daylight
+saving time.  Almost all of the Olson timezones are supported.")
     (license license:expat)))
 
 (define-public python2-pytz
   (package-with-python2 python-pytz))
 
+(define-public python-clyent
+  (package
+    (name "python-clyent")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "clyent" version))
+       (sha256
+        (base32
+         "1r9987qmy1pz3hq54160bapqsywpq14waw4w9x3ly8hmq7kpgfbj"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-mock" ,python-mock)))
+    (home-page "https://github.com/binstar/clyent")
+    (synopsis "Command line client library")
+    (description "Clyent is a Python command line utiliy library.  It is used
+by @code{binstar}, @code{binstar-build} and @code{chalmers}.")
+    (license license:bsd-3)))
+
+(define-public python2-clyent
+  (package-with-python2 python-clyent))
 
 (define-public python-babel
   (package
@@ -2715,6 +2741,46 @@ version numbers.")
              (propagated-inputs
               `(("python2-functools32" ,python2-functools32))))))
 
+(define-public python-schema
+  (package
+    (name "python-schema")
+    (version "0.6.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "schema" version))
+       (sha256
+        (base32
+         "1lw28j9w9vxyigg7vkfkvi6ic9lgjkdnfvnxdr7pklslqvzmk2vm"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page "https://github.com/keleshev/schema")
+    (synopsis "Simple data validation library")
+    (description
+     "@code{python-schema} is a library for validating Python data
+structures, such as those obtained from config-files, forms, external
+services or command-line parsing, converted from JSON/YAML (or
+something else) to Python data-types.")
+    (license license:psfl)))
+
+(define-public python2-schema
+  (package-with-python2 python-schema))
+
+(define-public python-schema-0.5
+  (package (inherit python-schema)
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "schema" version))
+       (sha256
+        (base32
+         "10zqvpaky51kgb8nd42bk7jwl8cn2zvayxjpdc1wwmpybj92x67s"))))))
+
+(define-public python2-schema-0.5
+  (package-with-python2 python-schema-0.5))
+
 (define-public python-kitchen
   (package
     (name "python-kitchen")
@@ -3125,6 +3191,36 @@ reStructuredText.")
 (define-public python2-pygments
   (package-with-python2 python-pygments))
 
+(define-public python-sphinxcontrib-websupport
+  (package
+    (name "python-sphinxcontrib-websupport")
+    (version "1.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "sphinxcontrib-websupport" version))
+              (sha256
+               (base32
+                "1f9f0wjpi9nhikbyaz6d19s7qvzdf1nq2g5dsh640fma4q9rd1bs"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("python-xapian-bindings" ,python-xapian-bindings)))
+    ;; Needed for running the test suite
+    (native-inputs
+     `(("python-six" ,python-six)
+       ("python-jinja2" ,python-jinja2)
+       ("python-docutils" ,python-docutils)
+       ("python-sphinx" ,python-sphinx)
+       ("python-sqlalchemy" ,python-sqlalchemy)
+       ("python-whoosh" ,python-whoosh)))
+    (home-page "http://sphinx-doc.org/")
+    (synopsis "Sphinx API for web applications")
+    (description "This package provides a Python API to easily integrate
+Sphinx documentation into your web application.  It provides tools to
+integrate Sphinx documents in web templates and to handle searches.")
+    (license license:bsd-3)))
+
 (define-public python-sphinx
   (package
     (name "python-sphinx")
@@ -3169,6 +3265,36 @@ sources.")
     (license license:bsd-3)
     (properties `((python2-variant . ,(delay python2-sphinx))))))
 
+(define-public python-sphinx-1.6
+  (package (inherit python-sphinx)
+    (name "python-sphinx")
+    (version "1.6.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "Sphinx" version))
+              (sha256
+               (base32
+                "1rj6f3i8hmrx2qlkshi5kp5xcy98dlynwlyl05yvflj5f66dp2xg"))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             ;; Requires Internet access.
+             (delete-file "tests/test_build_linkcheck.py")
+             (substitute* "tests/test_build_latex.py"
+               (("@pytest.mark.sphinx\\('latex', testroot='images'\\)")
+                "@pytest.mark.skip()"))
+             (zero? (system* "make" "test")))))))
+    (propagated-inputs
+     `(("python-sphinxcontrib-websupport" ,python-sphinxcontrib-websupport)
+       ,@(package-propagated-inputs python-sphinx)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest-3.0)
+       ("imagemagick" ,imagemagick) ; for "convert"
+       ,@(package-native-inputs python-sphinx)))
+    (properties '())))
+
 (define-public python-sphinx-1.5.3
   (package
     (inherit python-sphinx)
@@ -3684,7 +3810,39 @@ association studies (GWAS) on extremely large data sets.")
        ("pkg-config" ,pkg-config)
        ("python-sphinx" ,python-sphinx)
        ("python-numpydoc" ,python-numpydoc)
-       ("texlive" ,texlive)
+       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+                                        texlive-fonts-ec
+                                        texlive-generic-ifxetex
+                                        texlive-generic-pdftex
+                                        texlive-latex-amsfonts
+                                        texlive-latex-capt-of
+                                        texlive-latex-cmap
+                                        texlive-latex-environ
+                                        texlive-latex-eqparbox
+                                        texlive-latex-etoolbox
+                                        texlive-latex-expdlist
+                                        texlive-latex-fancyhdr
+                                        texlive-latex-fancyvrb
+                                        texlive-latex-fncychap
+                                        texlive-latex-float
+                                        texlive-latex-framed
+                                        texlive-latex-geometry
+                                        texlive-latex-graphics
+                                        texlive-latex-hyperref
+                                        texlive-latex-mdwtools
+                                        texlive-latex-multirow
+                                        texlive-latex-oberdiek
+                                        texlive-latex-parskip
+                                        texlive-latex-preview
+                                        texlive-latex-tabulary
+                                        texlive-latex-threeparttable
+                                        texlive-latex-titlesec
+                                        texlive-latex-trimspaces
+                                        texlive-latex-ucs
+                                        texlive-latex-upquote
+                                        texlive-latex-url
+                                        texlive-latex-varwidth
+                                        texlive-latex-wrapfig)))
        ("texinfo" ,texinfo)
        ("perl" ,perl)
        ("scipy-sphinx-theme"
@@ -3713,6 +3871,11 @@ association studies (GWAS) on extremely large data sets.")
                     (scipy-sphinx-theme "scipy-sphinx-theme")
                     (sphinx-theme-checkout (assoc-ref inputs scipy-sphinx-theme))
                     (pyver ,(string-append "PYVER=")))
+
+               ;; FIXME: this is needed to for texlive-union to generate
+               ;; fonts, which are not found.
+               (setenv "HOME" "/tmp")
+
                (with-directory-excursion "doc"
                  (copy-recursively sphinx-theme-checkout scipy-sphinx-theme)
                  (mkdir-p html)
@@ -4480,6 +4643,35 @@ multivalue dictionary that retains the order of insertions and deletions.")
 (define-public python2-furl
   (package-with-python2 python-furl))
 
+(define-public python-flaky
+  (package
+    (name "python-flaky")
+    (version "3.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "flaky" version))
+              (sha256
+               (base32
+                "18pkmf79rfkfpy1d2rrx3v55nxj762ilyk9rvd6s6dccxw58imsa"))))
+    (build-system python-build-system)
+    (arguments
+     ;; TODO: Tests require 'coveralls' and 'genty' which are not in Guix yet.
+     '(#:tests? #f))
+    (home-page "https://github.com/box/flaky")
+    (synopsis "Automatically rerun flaky tests")
+    (description
+     "Flaky is a plugin for @code{nose} or @code{py.test} that automatically
+reruns flaky tests.
+
+Ideally, tests reliably pass or fail, but sometimes test fixtures must rely
+on components that aren't 100% reliable.  With flaky, instead of removing
+those tests or marking them to @code{@skip}, they can be automatically
+retried.")
+    (license license:asl2.0)))
+
+(define-public python2-flaky
+  (package-with-python2 python-flaky))
+
 (define-public python-flask-babel
   (package
     (name "python-flask-babel")
@@ -5429,7 +5621,40 @@ tools for mocking system commands and recording calls to those.")
        ("python-nose" ,python-nose)
        ("python-sphinx" ,python-sphinx)
        ("python-shpinx-rtd-theme" ,python-sphinx-rtd-theme)
-       ("texlive" ,texlive)
+       ;; FIXME: It's possible that a smaller union would work just as well.
+       ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
+                                        texlive-fonts-ec
+                                        texlive-generic-ifxetex
+                                        texlive-generic-pdftex
+                                        texlive-latex-amsfonts
+                                        texlive-latex-capt-of
+                                        texlive-latex-cmap
+                                        texlive-latex-environ
+                                        texlive-latex-eqparbox
+                                        texlive-latex-etoolbox
+                                        texlive-latex-expdlist
+                                        texlive-latex-fancyhdr
+                                        texlive-latex-fancyvrb
+                                        texlive-latex-fncychap
+                                        texlive-latex-float
+                                        texlive-latex-framed
+                                        texlive-latex-geometry
+                                        texlive-latex-graphics
+                                        texlive-latex-hyperref
+                                        texlive-latex-mdwtools
+                                        texlive-latex-multirow
+                                        texlive-latex-oberdiek
+                                        texlive-latex-parskip
+                                        texlive-latex-preview
+                                        texlive-latex-tabulary
+                                        texlive-latex-threeparttable
+                                        texlive-latex-titlesec
+                                        texlive-latex-trimspaces
+                                        texlive-latex-ucs
+                                        texlive-latex-upquote
+                                        texlive-latex-url
+                                        texlive-latex-varwidth
+                                        texlive-latex-wrapfig)))
        ("texinfo" ,texinfo)))
     (arguments
      `(#:phases
@@ -6049,13 +6274,13 @@ of the structure, dynamics, and functions of complex networks.")
 (define-public snakemake
   (package
     (name "snakemake")
-    (version "3.11.2")
+    (version "3.13.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "snakemake" version))
        (sha256
-        (base32 "0qcp7y9csvanyzh08jppryhd5di8r1z7p0d4wkfg5591pj3bb8zp"))))
+        (base32 "1nixb944r4hlskwkzc4wjs34b40xpxpw9gmhhm5p09gvmm22ap5d"))))
     (build-system python-build-system)
     (arguments
      ;; TODO: Package missing test dependencies.
@@ -6337,6 +6562,31 @@ connection to each user.")
 (define-public python2-backports-abc
   (package-with-python2 python-backports-abc))
 
+(define-public python-backports-csv
+  (package
+    (name "python-backports-csv")
+    (version "1.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "backports.csv" version))
+       (sha256
+        (base32
+         "1imzbrradkfn8s2m1qcimyn74dn1mz2p3j381jljn166rf2i6hlc"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/ryanhiebert/backports.csv")
+    (synopsis "Backport of Python 3's csv module for Python 2")
+    (description
+     "Provides a  backport of Python 3's @code{csv} module for parsing
+comma separated values.  The API of the @code{csv} module in Python 2
+is drastically different from the @code{csv} module in Python 3.
+This is due, for the most part, to the difference between str in
+Python 2 and Python 3.")
+    (license license:psfl)))
+
+(define-public python2-backports-csv
+  (package-with-python2 python-backports-csv))
+
 (define-public python2-backports-shutil-get-terminal-size
   (package
     (name "python2-backports-shutil-get-terminal-size")
@@ -7392,14 +7642,14 @@ responses, rather than doing any computation.")
 (define-public python-cryptography-vectors
   (package
     (name "python-cryptography-vectors")
-    (version "1.9")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cryptography_vectors" version))
        (sha256
         (base32
-         "1wvq1p1viam1diz9x6d61x1bsy6cninv7cjgd35x9ffig9r6gxxv"))))
+         "0qadys01517k5wy0rifxip02p08kzrqxm5j0lmmlp0kr07h9jc7h"))))
     (build-system python-build-system)
     (home-page "https://github.com/pyca/cryptography")
     (synopsis "Test vectors for the cryptography package")
@@ -7414,14 +7664,14 @@ responses, rather than doing any computation.")
 (define-public python-cryptography
   (package
     (name "python-cryptography")
-    (version "1.9")
+    (version "2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cryptography" version))
        (sha256
         (base32
-         "10j8r1s29f4h59kp3mla14g588rm7qpn90nrczijk03i49q3662m"))))
+         "1c40qlxyn1jgg99f3pqi7146d3561rn9zdqc7w8f7kwr9ysm696k"))))
     (build-system python-build-system)
     (inputs
      `(("openssl" ,openssl)))
@@ -7463,16 +7713,14 @@ message digests and key derivation functions.")
 (define-public python-pyopenssl
   (package
     (name "python-pyopenssl")
-    (version "17.1.0")
+    (version "17.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyOpenSSL" version))
-       (patches
-        (search-patches "python-pyopenssl-17.1.0-test-overflow.patch"))
        (sha256
         (base32
-         "0qwmqhfsq84ydir9dz273ypmlcvs7v71m1jns0sd4k0h6lfsa82s"))))
+         "0d283g4zi0hr9papd24mjl70mi15gyzq6fx618rizi87dgipqqax"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -7496,7 +7744,8 @@ message digests and key derivation functions.")
     (inputs
      `(("openssl" ,openssl)))
     (native-inputs
-     `(("python-pretend" ,python-pretend)
+     `(("python-flaky" ,python-flaky)
+       ("python-pretend" ,python-pretend)
        ("python-pytest" ,python-pytest-3.0)))
     (home-page "https://github.com/pyca/pyopenssl")
     (synopsis "Python wrapper module around the OpenSSL library")
@@ -11641,53 +11890,6 @@ addresses, and phone numbers.")
        `(("python2-ipaddress" ,python2-ipaddress)
          ,@(package-propagated-inputs base))))))
 
-(define-public python-fake-factory
-  (package
-  (name "python-fake-factory")
-  (version "0.7.2")
-  (source (origin
-            (method url-fetch)
-            (uri (pypi-uri "fake-factory" version))
-            (sha256
-             (base32
-              "0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g"))
-            (patches
-             (search-patches
-              "python-fake-factory-fix-build-32bit.patch"))))
-  (build-system python-build-system)
-  (arguments
-   '(#:phases
-     (modify-phases %standard-phases
-       (replace 'check
-         (lambda _
-           (zero? (system* "python" "-m" "unittest" "-v" "faker.tests")))))))
-  (native-inputs
-   `(;; For testing
-     ("python-email-validator" ,python-email-validator)
-     ("python-mock" ,python-mock)
-     ("python-ukpostcodeparser" ,python-ukpostcodeparser)))
-  (propagated-inputs
-   `(("python-dateutil" ,python-dateutil)
-     ("python-six" ,python-six)))
-  (home-page "https://github.com/joke2k/faker")
-  (synopsis "Python package that generates fake data")
-  (description
-   "Faker is a Python package that generates fake data such as names,
-addresses, and phone numbers.")
-  (license license:expat)
-  (properties `((python2-variant . ,(delay python2-fake-factory))
-                (superseded . ,python-faker)))))
-
-(define-public python2-fake-factory
-  (let ((base (package-with-python2 (strip-python2-variant
-                                     python-fake-factory))))
-    (package
-      (inherit base)
-      (properties `((superseded . ,python2-faker)))
-      (propagated-inputs
-       `(("python2-ipaddress" ,python2-ipaddress)
-         ,@(package-propagated-inputs base))))))
-
 (define-public python-pyaml
   (package
     (name "python-pyaml")
@@ -14297,6 +14499,29 @@ pytest report.")
 (define-public python2-pytest-warnings
   (package-with-python2 python-pytest-warnings))
 
+(define-public python-pytest-capturelog
+  (package
+    (name "python-pytest-capturelog")
+    (version "0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-capturelog" version ".tar.gz"))
+       (sha256
+        (base32
+         "038049nyjl7di59ycnxvc9nydivc5m8np3hqq84j2iirkccdbs5n"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("pytest" ,python-pytest-3.0)))
+    (home-page "http://bitbucket.org/memedough/pytest-capturelog/overview")
+    (synopsis "Pytest plugin to catch log messages")
+    (description
+     "Python-pytest-catchlog is a pytest plugin to catch log messages.")
+    (license license:expat)))
+
+(define-public python2-pytest-capturelog
+  (package-with-python2 python-pytest-capturelog))
+
 (define-public python-pytest-catchlog
   (package
     (name "python-pytest-catchlog")
@@ -15173,6 +15398,49 @@ by path in a JSON document (see RFC 6901).")
 (define-public python2-jsonpointer
   (package-with-python2 python-jsonpointer))
 
+(define-public python-jsonpatch
+  (package
+    (name "python-jsonpatch")
+    (version "1.16")
+    (source
+     (origin
+       (method url-fetch)
+       ;; pypi version lacks tests.js
+       (uri (string-append "https://github.com/stefankoegl/python-json-patch/"
+                           "archive/v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "085ykisl8v7mv9h7hvhdy3l2fjzs4214gx32r5k6nx4f76hbv6y5"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-jsonpointer" ,python-jsonpointer)))
+    (home-page "https://github.com/stefankoegl/python-json-patch")
+    (synopsis "Applying JSON Patches in Python 2.6+ and 3.x")
+    (description "@code{jsonpatch} is a library and program that allows
+applying JSON Patches according to RFC 6902.")
+    (license license:bsd-3)))
+
+(define-public python2-jsonpatch
+  (package-with-python2 python-jsonpatch))
+
+(define-public python-jsonpatch-0.4
+  (package (inherit python-jsonpatch)
+    (name "python-jsonpatch")
+    (version "0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/stefankoegl/python-json-patch/"
+                           "archive/v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0j0cd9z9zyp8kppp464jxrfgrnbgkzl1yi10i5gsv8yz6d95929d"))))))
+
+(define-public python2-jsonpatch-0.4
+  (package-with-python2 python-jsonpatch-0.4))
+
 (define-public python-rfc3987
   (package
     (name "python-rfc3987")